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https://github.com/cellgeni/cloupe

Cloupe reader

https://github.com/cellgeni/cloupe

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.5%) to scientific vocabulary

Keywords

10x-genomics loupe reader single-cell
Last synced: 5 months ago · JSON representation

Repository

Cloupe reader

Basic Info
  • Host: GitHub
  • Owner: cellgeni
  • License: agpl-3.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 209 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
10x-genomics loupe reader single-cell
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

cloupe

Loupe Browser is a powerful visualization software that provides the intuitive functionality you need to explore and analyze 10x Genomics Chromium and Visium data. This is a PoC parser to read CLOUPE files using python.

Install

shell pip install git+https://github.com/cellgeni/cloupe.git

Run

```python from cloupe import Cloupe

parse file

c = Cloupe("/path/to/file.cloupe")

extract barcodes, features and projections to CSVs

c.to_csv(outdir="/path/to/out")

create anndata with the same name as input file but .h5ad extension

c.to_anndata() ```

Command line

Export barcodes, features and projections to CSV in current folder shell cloupe --cloupe /path/to/file.cloupe --csv

Owner

  • Name: Cellular Genetics Informatics
  • Login: cellgeni
  • Kind: organization
  • Location: United Kingdom

Wellcome Sanger Institute

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 6
  • Push event: 20
  • Pull request review comment event: 39
  • Pull request review event: 34
  • Pull request event: 2
  • Fork event: 2
  • Create event: 2
Last Year
  • Issues event: 2
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 6
  • Push event: 20
  • Pull request review comment event: 39
  • Pull request review event: 34
  • Pull request event: 2
  • Fork event: 2
  • Create event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • iaaka (2)
Pull Request Authors
  • NithinMathewJosephAston (1)
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